C. F. Negre, S. M. Mniszewski, M. J. Cawkwell, N. Bock, M. E. Wall, A. M. Niklasson. 2016. Recursive Factorization of the Inverse Overlap Matrix in Linear Scaling Quantum Molecular Dynamics Simulations. J Chem Theo Comput. In press.
M. E. Wall. 2016. Quantum crystallographic charge density of urea. IUCrJ 3, part 4. (Early View)
Anders M. N. Niklasson, Susan M. Mniszewski, Christian F. A. Negre, Marc J. Cawkwell, Pieter J. Swart, Jamal Mohd-Yusof, Timothy C. Germann, Michael E. Wall, Nicolas Bock, Emanuel H. Rubensson and Hristo Djidjev. 2016. Graph-based linear scaling electronic structure theory. J Chem Phys 144:234101. (URL)
A. H. Van Benschoten, L. Liu, A. Gonzalez, A. S. Brewster, N. K. Sauter, J. S. Fraser, M. E. Wall. 2016. Measuring and modeling diffuse scattering in protein X-ray crystallography. Proc Natl Acad Sci USA 113:4069. (pdf; URL)
N. Vesselinova, B. S. Alexandrov, M. E. Wall. 2015. Dynamical model of drug accumulation in bacteria: sensitivity analysis and experimentally testable predictions. Submitted. (bioRxiv)
I. Nemenman, M. E. Wall, C. E. M. Strauss. 2015. Of fishes and birthdays: Efficient estimation of polymer configurational entropies. Submitted. (arXiv)
S. M. Mniszewski, M. J. Cawkwell, M. E. Wall, J. Mohd-Yusof, N. Bock, T. C. Germann, and A. M. N. Niklasson. 2015. Efficient Parallel Linear Scaling Construction of the Density Matrix for Born–Oppenheimer Molecular Dynamics. J Chem Theo Comp 11:4644-4654. (URL)
A. H. Van Benschoten, P. V. Afonine, T. C. Terwilliger, M. E. Wall, C. J. Jackson, N. K. Sauter, P. D. Adams, A. Urzhumtsev, J. S. Fraser. 2015. Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles. Acta Crystallogr D Biol Crystallogr 71:1657-1667. (URL [open access]; PubMed)
M. E. Wall, A. H. Van Benschoten, N. K. Sauter, P. D. Adams, J. S. Fraser, T. C. Terwilliger. 2014. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering. Proc Natl Acad Sci USA 50:17887-17892. (pdf; PubMed)
M. E. Wall, P. D. Adams, J. S. Fraser, N. K. Sauter. 2014. Diffuse X-ray scattering to model protein motions. Structure 22:182-184. (URL; PubMed)
K. Verspoor, A. Mackinlay, J. D. Cohn, M. E. Wall. 2013. Detection of protein catalytic sites in the biomedical literature. Pacific Symposium on Biocomputing 18:433-444. (URL)
M. E. Wall, Ed., Quantitative Biology: From Molecular to Cellular Systems. Boca Raton: Chapman & Hall, 2012. (URL)
I. Nemenman, S. Gnanakaran, W. Hlavacek, Y. Jiang, B. Munsky, M. E. Wall, J. R. Faeder. 2012. The Fifth Annual q-bio Conference on Cellular Information Processing. Phys. Biol. 9:050201 (URL)
K. E. Ravikumar, H. Liu, J. D. Cohn, M. E. Wall, K. Verspoor. 2012. Literature mining of protein-residue associations with graph rules learned through distant supervision. J. Biomed. Semantics 3:S2. (URL)
K. M. Verspoor, J. D. Cohn, K. E. Ravikumar, M. E. Wall. 2012. Text mining improves prediction of protein functional sites. PLoS One 7:e32171. (URL)
D. Ming, M. E. Wall. 2012. Predicting binding sites by analyzing allosteric effects. Methods in Molecular Biology 796:423. (URL)
M. E. Wall, S. Raghavan, J. D. Cohn, J. Dunbar. 2011. Genome majority vote improves gene predictions. PLoS Computational Biology 7:e1002284. (URL)
I. Nemenman, J. R. Faeder, W. S. Hlavacek, Y. Jiang, M. E. Wall, A. Zilman. 2011. Selected papers from the Fourth Annual q-bio Conference on Cellular Information Processing. Physical Biology 8:050301. (URL)
M. E. Wall. 2011. Structure-function relations are subtle in genetic regulatory networks. Mathematical Biosciences 231:61. (URL)
J. Dunbar, J. D. Cohn, M. E. Wall. 2011. Consistency of gene starts among Burkholderia genomes. BMC Genomics 12:125. (URL)
I. Nemenman, W. S. Hlavacek, Y. Jiang, M. E. Wall, A. Zilman. 2010. The third q-bio conference on cellular information processing. IET Systems Biology 4:331. (PubMed)
M. E. Wall, D. A. Markowitz, J. L. Rosner, R. G. Martin. 2009. Model of transcriptional activation by MarA in Escherichia coli. PLoS Computational Biology 5:e1000614. (PubMed; URL)
M. E. Wall. 2009. Methods and software for diffuse X-ray scattering from protein crystals. Methods in Molecular Biology 544:269-279. (PubMed)
I. Nemenman, W. S. Hlavacek, Y. Jiang, M. E. Wall. 2009. Editorial: Selected papers from the Second q-bio Conference on Cellular Information Processing. IET Systems Biology 3:297. (PubMed)
D. W. Dreisigmeyer, J. Stajic, I. Nemenman, W. S. Hlavacek, M. E. Wall. 2008. Determinants of bistability in induction of the Escherichia coli lac operon. IET Systems Biology 2:293-303. (PubMed). Preprint (pdf).
I. Nemenman, W. S. Hlavacek, J. S. Edwards, J. R. Faeder, Y. Jiang, M. E. Wall. 2008. Selected papers from the First q-bio Conference on Cellular Information Processing. IET Systems Biology 2:203-205. (PubMed)
R. G. Martin, E. S. Bartlett, J. L. Rosner, M. E. Wall. 2008. Activation of the Escherichia coli marA/soxS/rob regulon in response to transcriptional activator concentration. J Mol Biol 380:278-284. (PubMed).
D. Ming, J. D. Cohn, M. E. Wall. 2008. Fast dynamics perturbation analysis for prediction of protein functional sites. BMC Structural Biology 8:5. (PubMed; URL).
D. Ming, M. Anghel, M. E. Wall. 2008. Hidden structure in protein energy landscapes. Phys. Rev. E. 77:021902. (PubMed). Preprint (pdf).
J. S. Edwards, J. R. Faeder, W. S. Hlavacek, Y. Jiang, I. Nemenman, M. E. Wall. 2007. q-bio 2007: a watershed moment in modern biology. Mol Syst Biol 3:148 (PubMed; URL)
I. Nemenman, G. S. Escola, W. S. Hlavacek, P. J. Unkefer, C. J. Unkefer, M. E. Wall. 2007. Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism. Ann NY Acad Sci 1115:102-115 (PubMed; pdf; arXiv:0706.2007).
D. Ming, M. E. Wall, K. Y. Sanbonmatsu. 2007. Domain motions of Argonaute, the catalytic engine of RNA interference. BMC Bioinformatics 8:470 (PubMed; URL)
M. E. Wall. 2006. Ligand Binding, Protein Fluctuations, and Allosteric Free Energy. AIP Conference Proceedings 851:16-33. Preprint (pdf). arXiv (q-bio.BM/0603027).
D. Ming, M. E. Wall. 2006. Interactions in native binding sites cause a large change in protein dynamics. J Mol Biol 358:213-223. (PubMed). Reprint (pdf). Preprint (pdf).
D. Ming, M. E. Wall. 2005. Allostery in a coarse-grained model of protein dynamics. Phys Rev Lett 95:198301. (PubMed; URL). Preprint (pdf). arXiv (q-bio.BM/0506031).
M.E. Wall, M.J. Dunlop, W.S. Hlavacek. 2005. Multiple functions of a feed-forward-loop gene circuit. J Mol Biol 349:501-514. (PubMed; URL); Preprint (pdf).
M.J. Dunlop, M.E. Wall. 2005. Robustness in Gene Circuits: Clustering of Functional Responses. Proceedings of the 2005 American Control Conference 6:4411-4416. Preprint (q-bio.MN/0503005).
D. Ming, M.E. Wall. 2005. Quantifying Allosteric Effects in Proteins. Proteins 59:697-707. (PubMed). Preprint (pdf). Early View (html).
M.E. Wall, W.S. Hlavacek, M.A. Savageau. 2004. Design of gene circuits: lessons from bacteria. Nat Rev Genet 5:34-42. (PubMed; pdf); Online table (pdf); EcoTFs web site (URL).
M.E. Wall, W.S. Hlavacek, M.A. Savageau. 2003. Design principles for regulator gene expression in a repressible gene circuit. J Mol Biol 332:861-876. (PubMed; pdf preprint)
M.E. Wall, S.H. Francis, J.D. Corbin, K. Grimes, R. Richie-Jannetta, J. Kotera, B.A. Macdonald, R.R. Gibson, J. Trewhella. 2003. Mechanisms associated with cGMP binding and activation of cGMP-dependent protein kinase. Proc Natl Acad Sci USA 100:2380-2385. (PubMed)
M.E. Wall, A. Rechtsteiner, L.M. Rocha. 2003. Singular Value Decomposition and Principal Component Analysis. In A Practical Approach to Microarray Data Analysis. D.P. Berrar, W. Dubitzky, M. Granzow, eds. pp. 91-109, Kluwer:Norwell, MA. (pdf; html)
M.E. Wall, P.A. Dyck, T.S. Brettin. 2001. SVDMAN – singular value decomposition analysis of microarray data. Bioinformatics 6:566-568. (PubMed)
M.E. Wall, S.C. Gallagher, J. Trewhella. 2000. Large-scale shape changes in proteins and macromolecular complexes. Ann Rev Phys Chem 51:355-380. (PubMed)
C.S. Tung, M.E. Wall, S.C. Gallagher and J. Trewhella. 2000. A model of troponin-I in complex with troponin-C using hybrid experimental data: the inhibitory region is a b-hairpin. Protein Sci 7:1312-1326 (cover article)(PubMed)
M.E. Wall, S. Subramaniam and G.N. Phillips, Jr. 1999. Protein structure determination using a database of interatomic distance probabilities. Protein Sci 8:2720-2727. (PubMed)
M.E. Wall, J.B. Clarage and G.N. Phillips, Jr. 1997. Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering. Structure 5:1599-1612. (PubMed)
M.E. Wall, S.E. Ealick and S.M. Gruner. 1997. Three-dimensional diffuse X-ray scattering from crystals of Staphylococcal nuclease. Proc Natl Acad Sci USA 94:6180-6184. (PubMed)
R.L. Walter, D.J. Thiel, S.L. Barna, M.W. Tate, M.E. Wall, E.F. Eikenberry, S.M. Gruner and S.E. Ealick. 1995. High-resolution macromolecular structure determination using CCD detectors and synchrotron radiation. Structure 3:835. (PubMed)
M.W. Tate, E.F. Eikenberry, S.L. Barna, M.E. Wall, J.L. Lowrance and S.M. Gruner. 1995. A large-format high-resolution area X-ray detector based on a fiber-optically bonded charge-coupled device (CCD). J Appl Cryst 28:196. (PubMed)
S.M. Gruner, S.L. Barna, M.E. Wall, M.W. Tate and E.F. Eikenberry. 1993. Characterization of polycrystalline phosphors for area X-ray detectors. SPIE Vol. 2009 X-ray Detector Physics and Applications II, 98. (SPIE)
Last modified Friday, 24-Jun-2016 09:22:12 MDT